Difference between revisions of "Data mining:WormMart:Example 1"

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(New page: === Example 1: List all synonyms for the following genes; bli-1, egl-43, lag-1 === * Start a new WormMart query: [http://www.wormbase.org/biomart/martview [HERE]]. * On the '''START''' p...)
 
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** Click the '''<export>''' button, which will load the results as shown on this [http://www.wormbase.org/biomart/martview/martview?outtype=feature&collection_gene_id=gene&collection_gene_id=public_name&collection_gene_id=name&outformat=html&outcompress=none&stage=output&collection_seq_scope_type_this=dna.transcript_exon_intron&schema=WS_CURRENT&default_link=---&gene_history_action=Acquires_merge&gene_gene_class=aak&gene_has_annotation_options=Only&dataset_last=gene&collection_molecular=seq_cds_name&seq_scope=tscr&gene_chromosome_name=I&status_count_filter=3&gene_ortholog_gene_last=Caenorhabditis%20briggsae&gene_utr_status_last=utr5%2Butr3&gene_ortholog_gene=Caenorhabditis%20briggsae&collection_gene=seq_wb_gene_id&collection_gene=seq_public_name&gene_id_list_options_last=public_name&gene_collection_id_list_toggle=1&gene_id_list_options_list=bli-1%2Cegl-43%2Clag-1&gene_species_selection=Brugia%20pahangi&default_link_last=---&gene_prediction_status=Confirmed&gene_history_action_last=Acquires_merge&collection_seq_scope_type=transcript_exon_intron&gene_id_list_options=public_name&gene_coding_status_last=coding&gene_chromosome_strand=-1&stage_initialised=start&stage_initialised=filter&stage_initialised=output&gene_utr_status=utr5%2Butr3&stage_prev=output&gene_chromosome_strand_last=-1&gene_prediction_status_last=Confirmed&gene_coding_status=coding&gene_identity_status=Dead&gene_has_annotation_options_last=Only&gene_chromosome_name_last=I&gene_species_selection_last=Brugia%20pahangi&gene_rnai_phenotype_options=Aberrant%20Cytoplasmic%20Structures&gene_has_annotation_options_filter=has_concise_description&collection_structure=exon_name&gene_rnai_phenotype_options_last=Aberrant%20Cytoplasmic%20Structures&gene_identity_status_last=Dead&dataset=gene&gene_gene_class_last=aak&status_count_start=44663&status_count_output=3&_export=1 [HERE]].
 
** Click the '''<export>''' button, which will load the results as shown on this [http://www.wormbase.org/biomart/martview/martview?outtype=feature&collection_gene_id=gene&collection_gene_id=public_name&collection_gene_id=name&outformat=html&outcompress=none&stage=output&collection_seq_scope_type_this=dna.transcript_exon_intron&schema=WS_CURRENT&default_link=---&gene_history_action=Acquires_merge&gene_gene_class=aak&gene_has_annotation_options=Only&dataset_last=gene&collection_molecular=seq_cds_name&seq_scope=tscr&gene_chromosome_name=I&status_count_filter=3&gene_ortholog_gene_last=Caenorhabditis%20briggsae&gene_utr_status_last=utr5%2Butr3&gene_ortholog_gene=Caenorhabditis%20briggsae&collection_gene=seq_wb_gene_id&collection_gene=seq_public_name&gene_id_list_options_last=public_name&gene_collection_id_list_toggle=1&gene_id_list_options_list=bli-1%2Cegl-43%2Clag-1&gene_species_selection=Brugia%20pahangi&default_link_last=---&gene_prediction_status=Confirmed&gene_history_action_last=Acquires_merge&collection_seq_scope_type=transcript_exon_intron&gene_id_list_options=public_name&gene_coding_status_last=coding&gene_chromosome_strand=-1&stage_initialised=start&stage_initialised=filter&stage_initialised=output&gene_utr_status=utr5%2Butr3&stage_prev=output&gene_chromosome_strand_last=-1&gene_prediction_status_last=Confirmed&gene_coding_status=coding&gene_identity_status=Dead&gene_has_annotation_options_last=Only&gene_chromosome_name_last=I&gene_species_selection_last=Brugia%20pahangi&gene_rnai_phenotype_options=Aberrant%20Cytoplasmic%20Structures&gene_has_annotation_options_filter=has_concise_description&collection_structure=exon_name&gene_rnai_phenotype_options_last=Aberrant%20Cytoplasmic%20Structures&gene_identity_status_last=Dead&dataset=gene&gene_gene_class_last=aak&status_count_start=44663&status_count_output=3&_export=1 [HERE]].
  
<br />[[Data_mining:WormMart Index of Examples] ... [[Data_mining:WormMart:Example_2 Next-&gt;]
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[[Data_mining:WormMart|Index of Examples]] ... [[Data_mining:WormMart:Example_2|Next-&gt;]]

Revision as of 03:17, 24 September 2007

Example 1: List all synonyms for the following genes; bli-1, egl-43, lag-1

  • Start a new WormMart query: [HERE].
  • On the START page;
    • Select the Gene dataset.
    • The <count> button on the right of the page will report the number of genes in the dataset in the Summary section, as shown [HERE].
    • Click <next> to proceed to the FILTER page.
  • On the FILTER page;
    • In the Identification section, enable the Limit to Gene ID(s) of Type - Public/CGC Name filter,
    • Paste the gene IDs bli-1, egl-43, lag-1 into the text box,
    • Click <count> to update the page, as shown [HERE]
    • Click <next> to proceed to the OUTPUT page.
  • On the OUTPUT page, in the IDENTIFICATION - IDs section;
    • Enable the Gene Public Name and Gene Names (merged) attributes as shown [HERE]
    • Click the <export> button, which will load the results as shown on this [HERE].
  • Note that the gene synonyms in the export are combined in a single table cell. To get a row per synonym rather than a row per gene;
    • Return to the OUTPUT page,
    • Disable the Gene Names (merged) attribute,
    • Enable the Gene Name (All) attribute,
    • Click the <export> button, which will load the results as shown on this [HERE].

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